The present invention provides a method for systematically controlling rapid proliferation of cyanobacteria cells in lakes in spring. The method applies physical, biological and chemical methods in an integrated and synergistic manner and includes using flexible enclosures to close a control water area and using modified soil to adsorb and settle algal cells; coupling four technologies including algae control by fish, algae control by biological floating islands, algae inhibition by plants and algae control by microorganisms; and using H2O2 to kill algae and using 40% FeCl3+CaCO3 and 50% Ca(NO3)2 to treat sediment. The method of the present invention has established a complete system for physical, chemical and biological control of algae, forms joint control of exogenous contaminants, endogenous contaminants and cyanobacteria, integrates physical, biological and chemical methods and optimizes systematic methods that are used synergistically.